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annotate cat.xml @ 25:cd83b5644eab draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc"
author bgruening
date Sat, 08 Oct 2022 20:59:15 +0000
parents 5fef6d08de83
children f22a309187a3
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1 <tool id="tp_cat" name="Concatenate datasets" version="0.1.1">
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2 <description>tail-to-head (cat)</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <version_command>
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8 <![CDATA[
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9 cat --version | head -n 1
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10 ]]>
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11 </version_command>
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12 <command>
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13 <![CDATA[
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14 #for $file in $inputs:
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15 cat '$file' >> '$out_file1' &&
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16 #end for
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17 #for $q in $queries:
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18 #for $file in $q.inputs2:
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19 cat '$file' >> '$out_file1' &&
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20 #end for
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21 #end for
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22 exit 0
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23 ]]></command>
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24 <inputs>
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25 <param name="inputs" multiple="true" type="data" format="txt,fastq.gz,fasta.gz,genbank.gz,tabular.gz" label="Datasets to concatenate"/>
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26 <repeat name="queries" title="Dataset">
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27 <param name="inputs2" type="data" format="txt,fastq.gz,fasta.gz,genbank.gz,tabular.gz" multiple="True" label="Select" />
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28 </repeat>
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29 </inputs>
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30 <outputs>
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31 <data name="out_file1" format_source="inputs" metadata_source="inputs"/>
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="inputs" value="sort_result1.bed,sort_result2.bed,sort_result3.bed"/>
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36 <output name="out_file1" file="cat_result1.txt"/>
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37 </test>
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38 <test>
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39 <param name="inputs" value="sort_result1.bed,sort_result3.bed"/>
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40 <repeat name="queries">
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41 <param name="inputs2" value="sort_result3.bed,sort_result3.bed"/>
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42 </repeat>
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43 <repeat name="queries">
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44 <param name="inputs2" value="sort_result3.bed"/>
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45 </repeat>
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46 <output name="out_file1" file="cat_result2.txt"/>
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47 </test>
8
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48 </tests>
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49 <help>
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50 <![CDATA[
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52 .. class:: warningmark
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54 **WARNING:** Be careful not to concatenate datasets of different kinds (e.g., sequences with intervals). This tool does not check if the datasets being concatenated are in the same format.
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56 -----
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58 **What it does**
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60 Concatenates datasets
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62 -----
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64 **Example**
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66 Concatenating Dataset::
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68 chrX 151087187 151087355 A 0 -
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69 chrX 151572400 151572481 B 0 +
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71 with Dataset1::
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73 chr1 151242630 151242955 X 0 +
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74 chr1 151271715 151271999 Y 0 +
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75 chr1 151278832 151279227 Z 0 -
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77 and with Dataset2::
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79 chr2 100000030 200000955 P 0 +
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80 chr2 100000015 200000999 Q 0 +
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82 will result in the following::
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84 chrX 151087187 151087355 A 0 -
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85 chrX 151572400 151572481 B 0 +
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86 chr1 151242630 151242955 X 0 +
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87 chr1 151271715 151271999 Y 0 +
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88 chr1 151278832 151279227 Z 0 -
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89 chr2 100000030 200000955 P 0 +
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90 chr2 100000015 200000999 Q 0 +
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92 @REFERENCES@
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93 ]]>
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94 </help>
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95 <expand macro="citations" />
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96 </tool>